EMBL to UCSC nib converter | SequenceConversion

Convert a EMBL sequence file to UCSC nib.

Convert from Convert to Choose your sequence file

Maximum file size: 50 MB. The file is checked before conversion.

EMBL → UCSC nib

This output format holds exactly one sequence. Upload a file with a single record.
UCSC nib stores only the DNA letters A, C, G, T, and N. Gaps, ambiguity codes, RNA (U), and protein letters are rejected.
UCSC nib does not store record names, so the output has no identifier.
The output keeps sequence records but drops features, references, and other source annotations.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.embl", "embl",
                      "output.nib", "nib")
print("Converted %i records" % count)

Sample input file: EMBL

Copy this example into a file, or download it, to try a EMBL conversion.

ID   EX000001; ; linear; DNA; ; PLN; 63 BP.
XX
AC   EX000001;
XX
DE   Example organism example gene, complete cds
XX
OS   Example organism
OC   .
XX
FH   Key             Location/Qualifiers
FH
FT   CDS             1..63
FT                   /gene="exampleA"
FT                   /product="example protein"
XX
SQ   Sequence 63 BP; 13 A; 13 C; 22 G; 15 T; 0 other;
     atggccattg taatgggccg ctgaaagggt gcccgatagt tcgcgattgt aatgggccgc        60
     tga                                                                      63
//

Download sample (sample.embl, 528 bytes)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

Choose another conversion